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Effect of host PCSK9 treatment on the gene expression of EO771 primary tumor

GSE255560 Mus musculus (mouse) Single-nucleus RNA-seq 15 samples Submitted 2024/12/09 Platform GPL16417
At a glance

Single-nucleus RNA-seq · mouse · 15 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
15 samples: 8 × EO771 tumor, Pcsk9 WT mouse, biol vs 7 × EO771 tumor, Pcsk9 KO mouse, biolGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
A commonly inherited human PCSK9 germline variant drives breast cancer metastasis via LRP1 receptorCell · 2025
Summary (written by the submitters)
Identifying patients at risk for metastatic relapse is a critical need in oncology. We identified a common missense germline variant in PCSK9 that associates with reduced breast cancer survival outcomes in multiple cohorts. Genetic modeling of this gain-of-function single nucleotide variant in mice revealed that it causally promoted breast cancer metastasis.
Read the full summary ↓
Conversely, host PCSK9 deletion reduced metastatic colonization in multiple breast cancer models. Host PCSK9 promoted metastatic initiation events in lung and increased proliferative competence by targeting tumoral LRP1 receptors which repress metastasis-promoting genes. Antibody-mediated therapeutic inhibition of PCSK9 suppressed breast cancer metastasis in multiple models. This variant stratified women in a large Swedish early-stage breast cancer cohort into those with 98% versus 78% distant-metastasis-free interval at 15 years after diagnosis. Our findings reveal that a commonly inherited genetic alteration predicts breast cancer survival and governs breast cancer metastasis—uncovering a hereditary basis underlying a prevalent cause of mortality.
Published in
A commonly inherited human PCSK9 germline variant drives breast cancer metastasis via LRP1 receptor
Mei W, Faraj Tabrizi S, Godina C et al. · Cell 2025 · PMID 39657676 · doi:10.1016/j.cell.2024.11.009
This dataset
Open GSE255560 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE255560_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1075437 and SRA study SRP489291. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39657676) ↗
Study design
8 × EO771 tumor, Pcsk9 WT mouse, biol vs 7 × EO771 tumor, Pcsk9 KO mouse, biol

Supports a between-group comparison across 15 samples.

How we read this: 2 replicated groups read from 15 sample titles; they account for 15 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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